index.qmd

---
title: BrainGlobe and napari
subtitle: Whole brain microscopy analysis
author: Adam Tyson, Alessandro Felder & Laura Porta
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# Welcome

## Schedule

### Morning
::: {.incremental}
* Installation (AT & AF)
* Introduction to BrainGlobe (AT)
* Introduction to napari (AF)
* Napari demo (AF)
* BrainGlobe & napari (AF) 
* Whole brain atlas registration & segmentation (AT)
:::

## Schedule

### Afternoon
::: {.incremental}
* 3D cell detection (AT)
* Analysing silicon probe tracks (AT)
* Analysing bulk fluorescence (AT)
* Using BrainGlobe in your own software (AF)
* Wrap up and Q&A (AT & AF)
:::

# Installation

{{< include slides/installation.qmd >}}

## Initial checkup

{{< include slides/mentimeter.qmd >}}

# BrainGlobe

{{< include slides/brainglobe-intro.qmd >}}
  

# [napari](https://napari.org/){preview-link="true" style="text-align: center"}

{{< include slides/napari-intro.qmd >}}

# napari demo

{{< include slides/napari-demo.qmd >}}

# Registration & segmentation

# Cell detection

# Silicon probe tracing

# Bulk fluorescence mapping

# BrainGlobe & your software

## BrainGlobe & your software
* Not just standalone tools
* Python APIs to help you build your own software
* Easy compatibility with other packages
* [Released tools](https://brainglobe.info/community/external-tools.html){preview-link="true"}

## Example script
* Find all hippocampal regions (`bg-atlasapi`)
* Display them in napari (`brainrender-napari`)

## Example script (demo)
```{.python}
import napari
from bg_atlasapi import BrainGlobeAtlas
from brainrender_napari.napari_atlas_representation import NapariAtlasRepresentation

# setup a napari viewer and a brainglobe atlas
viewer = napari.viewer.Viewer()
viewer.dims.ndisplay = 3 # set to 3d mode
atlas = BrainGlobeAtlas("allen_mouse_100um")

# find all hippocampal regions
hip_id = 1080 # the id of the hippocampus is 1080
hip_regions = [
    region["acronym"] 
    for region in atlas.structures_list 
    if hip_id in region["structure_id_path"]
]

# make a representation of the brainglobe atlas in napari
napari_atlas = NapariAtlasRepresentation(atlas, viewer)

# add all hippocampal regions to the napari viewer
for hip_region in hip_regions:
    napari_atlas.add_structure_to_viewer(hip_region)

# add the whole brain mesh as a help for orientation
napari_atlas.add_structure_to_viewer("root")

# run this script
if __name__ == "__main__":
    napari.run()
```

# Wrap up

## Resources
* [BrainGlobe website](https://brainglobe.info/){preview-link="true"}
* [Help forum](https://forum.image.sc/tag/brainglobe/){preview-link="true"}
* [Developer forum](https://brainglobe.zulipchat.com/){preview-link="true"}
* [GitHub](https://github.com/brainglobe/){preview-link="true"}

You are welcome to contribute to BrainGlobe - get in touch anytime and we will support you!

## Q+A

{{< include slides/mentimeter.qmd >}}

## Feedback

Please give us [some feedback](https://ideaboardz.com/for/BrainGlobe%20course%20feedback/5139784) on this pilot course.

# Thank you!